This command compares the structures in the given alignment.
It does not make an alignment, but it calculates the RMS and
DRMS deviations between atomic positions and distances, and class differences
between the mainchain and sidechain dihedral angles. In contrast to the
selection.superpose() command, alignment.compare_structures()
works with a multiple alignment and it writes more information about the
pairwise comparisons.

output selects short ('SHORT') or long ('LONG')
form of output to the log file. If it contains word
'RMS' or 'DRMS' it also outputs the RMS or DRMS deviation matrix
to file matrix_file. This file can be used with the
PHYLIP program or with the environ.dendrogram() or
environ.principal_components()
commands of MODELLER to calculate a clustering of the structures.

compare_mode selects the form of the positional variability
calculated for each position along the sequence:

1,

for true RMS deviation over all proteins that have a residue at
the current position. This does not make any sense for periodic quantities
like dihedral angles.

2,

for the average absolute distance over all pairs of
residues that have a residue at the current position.

3,

the same as 2 except that average distance, not its
absolute value is used (convenient for comparison of 2 structures to
get the
sign of the changes for dihedral angles and distances).

rms_cutoffs specifies cutoff values for calculation of the
position, distance, and dihedral angle RMS deviations for pairwise
overall comparisons. If difference between two equivalent points is
larger than cutoff it is not included in the RMS sum. The order of
cutoffs in this vector is: atomic position, intra-molecular distance,
α
, Φ
, Ψ
, ω
, χ1
, χ2
, χ3
, χ4
,
and χ5
(there are 5 dihedrals in a disulfide bridge), where
α
is the virtual
Cα
dihedral angle between four consecutive
Cα
atoms. These cutoffs do not affect positional variability
calculations.

fit_atoms string specifies all the atom types (including possibly
a generic 'ALL') to be fitted in the least-squares superposition.
These atom types are used in the least-squares superposition, and in
calculation of the position and distance RMS deviations.

varatom specifies the atom type that is used for
getting the average structure and RMS deviation at each alignment position in
the ASGL output file 'posdif.asgl'. This ASGL file contains the
positional variability of the selected atom type in the family of
compared proteins. The ASGL output files can then be used with
ASGL scripts 'posdif' and 'dih' to produce POSTSCRIPT plots of the
corresponding variabilities at each alignment position.
asgl_output has to be True to obtain the ASGL output files.

If fit = True, a least-squares superposition is done before the
comparisons; otherwise, the orientation of the molecules in the
input atom files is used.